Did you work with a Cisco Meraki partner on the design for this network before it got deployed, or did you do the design yourself based on what you already had?
I think your issues relates to the design chosen (model of switches chosen, quantities and stack design).
If you were my customer, I would have recommended using the classic collapsed core/distribution layer, and a separate access layer. This design is documented here (although Meraki calls it aggregation rather than distribution, but same thing).
https://meraki.cisco.com/lib/pdf/meraki_campus_deployment_guide.pdf
For the collapsed core/distribution I would have used a stacked pair of MS425 switches (which only have 10Gbe ports).
https://meraki.cisco.com/products/switches/ms425-16
From what you describe, I would then plug all the storage and servers into this. If you had a lot of servers/storage I would deploy another separate pair of MS425's for a dedicated server access layer, but it doesn't sound like you have enough to make this worthwhile.
Then for the access layer I would have used MS225's, and formed 10Gbe Etherchannels back to the core switches.
https://meraki.cisco.com/products/switches/ms225-48
I would have limited the stack sizes to 4 but preferred a smaller stack size of 3 were possible, which each stack having its own 10Gbe Etherchannel uplink. I would have used a limit of 4 because my prior experience tells me this is rock solid reliable, and because I would like to limit the over subscription rate of the upstream links:
- a stack of 3 x 48 ports with dual 10Gbe uplinks is 144Gb into 20Gb for a 7:1 oversubscription
- a stack of 4 x 48 ports with dual 10Gbe uplinks is 192Gb into 20Gb for a 10:1 oversubscription
- a stack of 6 x 48 ports with dual 10Gbe uplinks is 288Gb into 20Gb for a 14:1 oversubscription
You can see two stacks of 3 switches will deliver twice the performance out of the access layer as a single stack of 6 switches. You can see how this design discourages you from stacking high, because you limit performance - and the cost is the same - so why would you?
I would also have given you a guarantee that the deployment would be rock solid reliable with no performance issues.